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Informatics

Duncan Hull
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  • September 9, 2014
  • 06:03 AM
  • 143 views

Punning with the Pub in PubMed: Are there any decent NCBI puns left? #PubMedPuns

by Duncan Hull in O'Really?

Many people claim they get all their best ideas in the Pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, many puns and portmanteaus (aka “PubManteaus”), the pub-based wordplays are very common. All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete coll........ Read more »

Gibney Elizabeth. (2014) How to tame the flood of literature. Nature, 513(7516). PMID: 25186906  

Kumar Neeraj, Berg Alexander, Belhumeur Peter N, & Nayar Shree. (2011) Describable Visual Attributes for Face Verification and Image Search. IEEE transactions on pattern analysis and machine intelligence. PMID: 21383395  

McEntyre Johanna R, Ananiadou Sophia, Andrews Stephen, Black William J, Boulderstone Richard, Buttery Paula, Chaplin David, Chevuru Sandeepreddy, Cobley Norman, & Coleman Lee-Ann. (2010) UKPMC: a full text article resource for the life sciences. Nucleic acids research. PMID: 21062818  

  • July 29, 2014
  • 05:00 PM
  • 178 views

A simple and useable classification of software by Aral Balkan via Wuthering Bytes

by Duncan Hull in O'Really?

It’s getting pretty hard to do anything these days that doesn’t involve software. Our governments, businesses, laboratories, personal lives and entertainment would look very different without the software that makes them tick. How can we classify all this software to make sense of it all? The likes of this huge list of software categories on wikipedia are pretty bewildering, and projects such as the Software Ontology (SWO) [1] are attempting to make sense of swathes of software too. ........ Read more »

  • August 7, 2013
  • 07:17 AM
  • 416 views

A taste of beekeeping with @Grow4ItChorlton in Chorlton-cum-Honey

by Duncan Hull in O'Really?

Down in deepest, darkest Chorlton-cum-Hardy [1] the good people of Grow for it Chorlton have been running a series of taster sessions on beekeeping (a.k.a. apiculture). Here’s some notes from one of these sessions held last weekend and some info on where to find out more if you’re interested.... Read more »

  • June 18, 2013
  • 06:16 AM
  • 490 views

Peter Suber’s Open Access book is now available under an #OpenAccess license

by Duncan Hull in O'Really?

If you never got around to buying Peter Suber‘s book “for busy people” about Open Access (OA) publishing [1], you might be pleased to learn that it’s now available under an Open Access license.... Read more »

  • May 14, 2013
  • 02:00 AM
  • 297 views

Measuring scientific coverage of @Wikipedia: Fellows of the Wiki Society Index 2013

by Duncan Hull in O'Really?

A quick-and-dirty measure of the scientific coverage of wikipedia is the percentage of these fellows that have a profile on wikipedia at the time of their election to the prestigous Society. Let’s call it the Fellows of the Wiki Society Index (FWSi)...... Read more »

Moy, C., Locke, J., Coppola, B., & McNeil, A. (2010) Improving Science Education and Understanding through Editing Wikipedia. Journal of Chemical Education, 87(11), 1159-1162. DOI: 10.1021/ed100367v  

  • January 17, 2013
  • 01:54 PM
  • 534 views

How to export, delete and replace your Mendeley account and library

by Duncan Hull in O'Really?

News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1], so it will be interesting to see how this plays out.

If you’ve built a personal library of sci........ Read more »

  • January 11, 2013
  • 11:59 AM
  • 546 views

A joke about teaching and learning via Jason Bangbala

by Duncan Hull in O'Really?

What is the difference between primary, secondary and higher education?... Read more »

Vardi, M. (2012) Will MOOCs destroy academia?. Communications of the ACM, 55(11), 5-5. DOI: 10.1145/2366316.2366317  

Khan, S. (2013) What college could be like. Communications of the ACM, 56(1), 41. DOI: 10.1145/2398356.2398370  

  • December 21, 2012
  • 11:59 AM
  • 259 views

Happy Christmas Lectures (Merry “Chemist-mas” everyone)

by Duncan Hull in O'Really?

If you hate Chemistry [1] it’s probably because your Chemistry teachers weren’t up to scratch. Peter Wothers, The Modern Alchemist, is someone who might rekindle your interest in Chemistry through his delivery of the 2012 Christmas Lectures. Wothers will unpick the chemistry of the world around us, looking at Air, Water and Earth, three of the original Greek ‘elements’ that tantalised alchemists for centuries. He’ll also be exploding and burning things too.... Read more »

Lippincott, W. (1979) Why Students Hate Chemistry. Journal of Chemical Education, 56(1), 1. DOI: 10.1021/ed056p1  

  • November 30, 2012
  • 09:16 AM
  • 432 views

The University of Mo-chester, UK: Scientific Movember Team

by Duncan Hull in O'Really?

Movember is now in its tenth year but like many men, I’ve resisted the urge to grow a Mo because of

an inability to grow a decent moustache
a reluctance to look like a p0rn star / seventies pervert / gay cowboy [delete as appropriate]
a fear of scaring off potential collaborators, customers, undergraduates, postgraduates, friends etc
a long history of fine facial foliage from Errol Flynn to Tom Selleck, Henry Wellcome to Freddie Mercury, Charlie Chaplin to Lemmy from Motörhead. ........ Read more »

McCartney, M. (2012) Is Movember misleading men?. BMJ, 345(nov28 1). DOI: 10.1136/bmj.e8046  

Jeffcott, M., Cagiannos, I., & Zorn, K. (2012) Movember update: The Canadian perspective. Canadian Urological Association Journal, 6(3). DOI: 10.5489/cuaj.12037  

  • September 26, 2012
  • 08:50 AM
  • 336 views

Fellows of the Wiki Society? The Royal Society in London experiments with Wikipedia

by Duncan Hull in O'Really?

Venerable and learned society experiments with wikipedia... Read more »

Wodak Shoshana J., Mietchen Daniel, Collings Andrew M., Russell Robert B., & Bourne Philip E. (2012) Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology, 8(3). DOI: 10.1371/journal.pcbi.1002446  

  • August 20, 2012
  • 08:09 AM
  • 657 views

Digital Research 2012: September 10th-12th St Catherine’s College, Oxford, UK

by Duncan Hull in O'Really?

The UK’s premier Digital Research community event is being held in Oxford 10-12 September 2012. Come along to showcase and share the latest in digital research practice – and set the agenda for tomorrow at Digital Research 2012. The conference features an exciting 3-day programme with a great set of invited speakers together with showcases of the work and vision of the Digital Research community. Here are some highlights of the programme – please see the website digital-researc........ Read more »

Lazer D., Pentland A., Adamic L., Aral S., Barabasi A.-L., Brewer D., Christakis N., Contractor N., Fowler J., & Gutmann M. (2009) SOCIAL SCIENCE: Computational Social Science. Science, 323(5915), 723. DOI: 10.1126/science.1167742  

  • August 17, 2012
  • 06:20 AM
  • 734 views

What is the collective noun for a group of Systems Biologists?

by Duncan Hull in O'Really?

What happened was, I was looking for a Creatively Commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. That’s not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at t........ Read more »

Lander Arthur D. (2010) The edges of understanding. BMC Biology, 8(1). DOI: 10.1186/1741-7007-8-40  

Kitano Hiroaki. (2002) Systems Biology: A Brief Overview. Science, 295(5560), 1664. DOI: 10.1126/science.1069492  

Ideker Trey, Galitski Timothy, & Hood Leroy. (2001) Systems Biology: A new approach to decoding life . Annual Review of Genomics and Human Genetics, 2(1), 372. DOI: 10.1146/annurev.genom.2.1.343  

  • August 3, 2012
  • 03:47 AM
  • 559 views

Where did all the BBC programme metadata go? The infax catalogue online

by Duncan Hull in O'Really?

Over at @BBCSport and @BBC2012 there are some Olympian feats of big data wrestling going on behind the scenes for London 2012 [1]. While we all enjoy the Olympics on a range of platforms and devices, a team of twenty engineers is busy making it all happen. It’s great that the BBC, unlike other large organisations, can talk openly about their technology and share hard-won knowledge widely.... Read more »

  • July 27, 2012
  • 03:35 AM
  • 717 views

Olympic Science: The Long Jump to Conclusions

by Duncan Hull in O'Really?

If Science were an Olympic sport, which events would scientists excel at?... Read more »

Cressey Daniel, & Callaway Ewen. (2012) Science at the Olympics: Team science. Nature, 487(7407), 292. DOI: 10.1038/487290a  

Noakes Timothy, & Spedding Michael. (2012) Olympics: Run for your life. Nature, 487(7407), 296. DOI: 10.1038/487295a  

Enriquez Juan, & Gullans Steve. (2012) Olympics: Genetically enhanced Olympics are coming. Nature, 487(7407), 297. DOI: 10.1038/487297a  

Loza-Coll Mariano A. (2012) Piled too high. Nature, 486(7403), 431. DOI: 10.1038/nj7403-431a  

  • June 29, 2012
  • 02:35 AM
  • 743 views

Impact Factor Boxing 2012

by Duncan Hull in O'Really?

In the world of abused performance metrics, the impact factor is the undisputed heavyweight champion of the (publishing) world.

And it’s been an eventful year in the ring scientific publishing too. A new journal called PeerJ launched with a radical new publish ’til you perish business model [1]. There’s another new journal on the way too in the shape of eLifeSciences - with it’s own significant differences from current publishing models. Then there was the Finch report........ Read more »

  • June 15, 2012
  • 10:49 AM
  • 633 views

Alan Turing Centenary Conference, 22nd-25th June 2012

by Duncan Hull in O'Really?

Next weekend, a bunch of very distinguished computer scientists will rock up at the magnificent Manchester Town Hall for the Turing Centenary Conference in order to analyse the development of Computer Science, Artificial Intelligence and Alan Turing’s legacy [1].... Read more »

  • June 1, 2012
  • 08:00 AM
  • 757 views

An Open Letter to the Royal Society: Please employ a wikipedian in residence

by Duncan Hull in O'Really?

Fellows of the Wiki Society? To improve public engagement with Science and Scientists, the Royal Society should employ a wikipedian in residence. Here’s why:... Read more »

Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008) The RNA WikiProject: Community annotation of RNA families. RNA, 14(12), 2462-2464. DOI: 10.1261/rna.1200508  

Wodak, S., Mietchen, D., Collings, A., Russell, R., & Bourne, P. (2012) Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology, 8(3). DOI: 10.1371/journal.pcbi.1002446  

  • May 24, 2012
  • 03:57 AM
  • 826 views

Physics or Stamp Collecting? Let’s hear it for the Stamp Collectors

by Duncan Hull in O'Really?

The Life Scientific is a series of interviews by Jim Al-Khalili of well known scientists. It’s a bit like Desert Island Discs without the music and with more interesting guests. If you missed them on the radio, you can download the lot as a podcast. Here’s a good example of an interview with John Sulston on the Physics vs. Stamp Collecting debate:... Read more »

  • May 18, 2012
  • 04:54 AM
  • 883 views

Web analytics: Numbers speak louder than words

by Duncan Hull in O'Really?

According to the software which runs this site, this is the 200th post here at O’Really? To mark the occasion, here are some stats via WordPress with thoughts and general navel-gazing analysis paralysis [1] on web analytics. It all started just over six years ago at nodalpoint with help from Greg Tyrelle, the last four years have been WordPressed with help from Matt Mullenwegg. WordPress stats are unfortunately very primitive compared to the likes of Google Analytics and don’t give ........ Read more »

  • May 11, 2012
  • 09:58 AM
  • 638 views

Journal Fire: Bonfire of the Vanity Journals?

by Duncan Hull in O'Really?

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire is the burning effigy of a wicker man, representing the very worst of the vanity journals.... Read more »

Deans Andrew R., Yoder Matthew J., & Balhoff James P. (2012) Time to change how we describe biodiversity. Trends in Ecology , 27(2), 84. DOI: 10.1016/j.tree.2011.11.007  

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